Antigen

Antigen Class

TFs and others

Antigen

Cebpb

Cell type

Cell type Class

Neural

Cell type

Microglia

MeSH Description

The third type of glial cell, along with astrocytes and oligodendrocytes (which together form the macroglia). Microglia vary in appearance depending on developmental stage, functional state, and anatomical location; subtype terms include ramified, perivascular, ameboid, resting, and activated. Microglia clearly are capable of phagocytosis and play an important role in a wide spectrum of neuropathologies. They have also been suggested to act in several other roles including in secretion (e.g., of cytokines and neural growth factors), in immunological processing (e.g., antigen presentation), and in central nervous system development and remodeling.

Sample

source_name

Primary microglia

background

C57BL/6

age

P0-P2

genotype

Cop1 WT

cell type

Microglia

chip antibody

c/EBP<beta> (Santa Cruz H-7)

Sequenced DNA Library

library_strategy

ChIP-Seq

library_source

GENOMIC

library_selection

ChIP

library_construction_protocol

Primary microglia were isolated from newborn mouse brains (P0-P2) as described (Lian et al., 2016). Briefly, hippocampi and cortices were mechanically dissociated and meninges removed with a 70 µm filter. Single cell suspensions from 4-5 brains were pooled in T-225 flasks (Corning) in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% heat inactivated fetal bovine serum, 2 mM glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin (Gibco). The culture media was changed the next day to remove cell debris. After 10-14 days of culture, microglia were collected by shaking the flask at 110 rpm for 1 h. Microglia were plated on non-treated plates. The next day they were treated with 0.1 μM 4-hydroxytamoxifen (4-OHT, Sigma-Aldrich) for 48 h. Active Motif Epigenetic services performed ChIP assays. Cells fixed with 1% formaldehyde for 11 min were quenched with 0.25 M glycine and then were swollen in lysis buffer for 30 min on ice. Chromatin was isolated after sonication to shear the DNA to an average length of 300–500 bp. Input and immunoprecipitated DNAs were treated with RNase, proteinase K, and heat for de-crosslinking, followed by ethanol precipitation. Antibodies used for immunoprecipitation were c/EBPß (Santa Cruz H-7), H3K4me3 (Abcam ab8580) and H2K27ac (Abcam ab4729). Libraries were prepared using standard protocols for the Ovation Ultralow System. Briefly, samples were PCR-amplified and sized using the Agilent 2100Bioanalyzer. Barcoded libraries were sequenced 75 bp single end on HiSeq 2500 (Illumina).

Sequencing Platform

instrument_model

Illumina HiSeq 2500

mm10

Number of total reads

36429001

Reads aligned (%)

93.2

Duplicates removed (%)

36.5

Number of peaks

6748 (qval < 1E-05)

mm9

Number of total reads

36429001

Reads aligned (%)

93.1

Duplicates removed (%)

36.6

Number of peaks

6760 (qval < 1E-05)